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Liang W, Du H, Pang B, Cheng J, He B, Hu F, Lv Y, Zhang Y. High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1076600. [PMID: 36618635 PMCID: PMC9822775 DOI: 10.3389/fpls.2022.1076600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.
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Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Leng Y, Zhao M, Fiedler J, Dreiseitl A, Chao S, Li X, Zhong S. Molecular Mapping of Loci Conferring Susceptibility to Spot Blotch and Resistance to Powdery Mildew in Barley Using the Sequencing-Based Genotyping Approach. PHYTOPATHOLOGY 2020; 110:440-446. [PMID: 31609681 DOI: 10.1094/phyto-08-19-0292-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spot blotch (SB) caused by Bipolaris sorokiniana and powdery mildew (PM) caused by Blumeria graminis f. sp. hordei are two important diseases of barley. To map genetic loci controlling susceptibility and resistance to these diseases, a mapping population consisting of 138 recombinant inbred lines (RILs) was developed from the cross between Bowman and ND5883. A genetic map was constructed for the population with 852 unique single nucleotide polymorphism markers generated by sequencing-based genotyping. Bowman and ND5883 showed distinct infection responses at the seedling stage to two isolates (ND90Pr and ND85F) of Bipolaris sorokiniana and one isolate (Race I) of Blumeria graminis f. sp. hordei. Genetic analysis of the RILs revealed that one major gene (Scs6) controls susceptibility to Bipolaris sorokiniana isolate ND90Pr, and another major gene (Mla8) confers resistance to Blumeria graminis f. sp. hordei isolate Race I, respectively. Scs6 was mapped on chromosome 1H of Bowman, as previously reported. Mla8 was also mapped to the short arm of 1H, which was tightly linked but not allelic to the Rcs6/Scs6 locus. Quantitative trait locus (QTL) analysis identified two QTLs, QSbs-1H-P1 and QSbs-7H-P1, responsible for susceptibility to spot blotch caused by Bipolaris sorokiniana isolate ND85F in ND5883, which are located on chromosome 1H and 7H, respectively. QSbs-7H-P1 was mapped to the same region as Rcs5, whereas QSbs-1H-P1 may represent a novel allele conferring seedling stage susceptibility to isolate ND85F. Identification and molecular mapping of the loci for SB susceptibility and PM resistance will facilitate development of barley cultivars with resistance to the diseases.
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Affiliation(s)
- Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Mingxia Zhao
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Jason Fiedler
- Department of Plant Science, North Dakota State University, Fargo, ND 58102, U.S.A
- U.S. Department of Agriculture-Agriculture Research Service Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | | | - Shiaoman Chao
- U.S. Department of Agriculture-Agriculture Research Service Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | - Xuehui Li
- Department of Plant Science, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
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Liu H, Zhang L, Wang J, Li C, Zeng X, Xie S, Zhang Y, Liu S, Hu S, Wang J, Lee M, Lübberstedt T, Zhao G. Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population. FRONTIERS IN PLANT SCIENCE 2017; 8:813. [PMID: 28588594 PMCID: PMC5439002 DOI: 10.3389/fpls.2017.00813] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/01/2017] [Indexed: 05/09/2023]
Abstract
Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51-7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize.
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Affiliation(s)
- Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Lin Zhang
- Department of Agronomy, Northeast Agricultural UniversityHarbin, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Changsheng Li
- Department of Agronomy, Shenyang Agricultural UniversityShenyang, China
| | - Xing Zeng
- Department of Agronomy, Northeast Agricultural UniversityHarbin, China
| | - Shupeng Xie
- Suihua Sub-academy, Heilongjiang Academy of Agricultural SciencesSuihua, China
| | - Yongzhong Zhang
- Department of Plant Genetics and Breeding, College of Agronomy Sciences, Shandong Agricultural UniversityTai'an, China
| | - Sisi Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Songlin Hu
- Department of Agronomy, Iowa State UniversityAmes, IA, United States
| | - Jianhua Wang
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural UniversityBeijing, China
| | - Michael Lee
- Department of Agronomy, Iowa State UniversityAmes, IA, United States
| | | | - Guangwu Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry UniversityLin'an, China
- *Correspondence: Guangwu Zhao
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Chen L, Gao W, Chen S, Wang L, Zou J, Liu Y, Wang H, Chen Z, Guo T. High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. RICE (NEW YORK, N.Y.) 2016; 9:48. [PMID: 27659284 PMCID: PMC5033801 DOI: 10.1186/s12284-016-0121-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study. RESULTS A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization. CONCLUSION QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.
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Affiliation(s)
- Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Weiwei Gao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Liping Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiyong Zou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Agricultural Technology Extension, Guangzhou, 510520, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Liu H, Soomro A, Zhu Y, Qiu X, Chen K, Zheng T, Yang L, Xing D, Xu J. QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice ( Oryza sativa L.). ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zhang Q, Zheng T, Hoang L, Wang C, Nafisah, Joseph C, Zhang W, Xu J, Li Z. Joint Mapping and Allele Mining of the Rolled Leaf Trait in Rice (Oryza sativa L.). PLoS One 2016; 11:e0158246. [PMID: 27441398 PMCID: PMC4956317 DOI: 10.1371/journal.pone.0158246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/12/2016] [Indexed: 01/01/2023] Open
Abstract
The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI. Five of these loci were previously identified and two (qRl7b and qRl9b) are newly reported with additional evidence from GWAS mapping for qRl7b. A total of 18 QTLs were identified by GWAS, including four newly identified QTLs. Six QTLs were confirmed by linkage mapping with the above RIL population, and 83.3% were found to be consistent with previously reported loci based on comparative mapping. We also performed allele mining with representative SNPs and identified the elite germplasms for the improvement of rolled leaf trait. Most favorable alleles at the detected loci were contributed by various 3K Rice germplasms. By a re-scanning of the candidate region with more saturated SNP markers, we dissected the region harboring gRl4-2 into three subregions, in which the average effect on LRI was 3.5% with a range from 2.4 to 4.1% in the third subregion, suggesting the presence of a new locus or loci within this region. The representative SNPs for favorable alleles in the reliable QTLs which were consistently identified in both bi-parental mapping and GWAS, such as qRl4, qRl5, qRl6, qRl7a, and qRl7b will be useful for future molecular breeding programs for ideal plant type in rice.
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Affiliation(s)
- Qiang Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Long Hoang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Chunchao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Nafisah
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Charles Joseph
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Wenzhong Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Wang T, Wang M, Hu S, Xiao Y, Tong H, Pan Q, Xue J, Yan J, Li J, Yang X. Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population. BMC PLANT BIOLOGY 2015; 15:288. [PMID: 26654531 PMCID: PMC4676831 DOI: 10.1186/s12870-015-0675-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Starch from maize kernels has diverse applications in human and animal diets and in industry and manufacturing. To meet the demands of these applications, starch quantity and quality need improvement, which requires a clear understanding of the functional mechanisms involved in starch biosynthesis and accumulation. In this study, a recombinant inbred line (RIL) population was developed from a cross between inbred lines CI7 and K22. The RIL population, along with both parents, was grown in three environments, and then genotyped using the MaizeSNP50 BeadChip and phenotyped to dissect the genetic architecture of starch content in maize kernels. RESULTS Based on the genetic linkage map constructed using 2,386 bins as markers, six quantitative trait loci (QTLs) for starch content in maize kernels were detected in the CI7/K22 RIL population. Each QTL accounted for 4.7% (qSTA9-1) to 10.6% (qSTA4-1) of the starch variation. The QTL interval was further reduced using the bin-map method, with the physical distance of a single bin at the QTL peak ranging from 81.7 kb to 2.2 Mb. Based on the functional annotations and prior knowledge of the genes in the top bin, seven genes were considered as potential candidate genes for the identified QTLs. Three of the genes encode enzymes in non-starch metabolism but may indirectly affect starch biosynthesis, and four genes may act as regulators of starch biosynthesis. CONCLUSIONS A few large-effect QTLs, together with a certain number of minor-effect QTLs, mainly contribute to the genetic architecture of kernel starch content in our maize biparental linkage population. All of the identified QTLs, especially the large-effect QTL, qSTA4-1, with a small QTL interval, will be useful for improving the maize kernel starch content through molecular breeding.
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Affiliation(s)
- Tingting Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
| | - Min Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Shuting Hu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
| | - Yingni Xiao
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
| | - Hao Tong
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Qingchun Pan
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Jiquan Xue
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Jiansheng Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.
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